Nucleic acids are an essential component of biological systems. We have a long-standing interest in modeling DNA and RNA, but also technologically relevant peptide-nucleic acid systems.
In previous work we have focused on the functional dynamics of protein-nucleic complexes such as RNA polymerase II and the MutS mismatch repair system. We have also developed models of chromosomal DNA driven by experimental data.
Our current interests related to nucleic acids involve:
- Role of RNA in biomolecular condensate formation
- Interactions between proteins and nucleic acids under crowded conditions
- Internal dynamics of folded RNA structures
We study nucleic acids via coarse-grained and atomistic simulations. The COCOMO model developed by us includes parameters for RNA and allows the study of peptide-RNA condensates.
Software and modeling resources:
- COCOMO: nucleotide-level coarse-grained model of RNA
